How to change UVMap index?
According to the blender 2.69 python API reference, uv_textures is a bpy_prop_collection of MeshTexturePolyLayer and it is read only. It would appear to be accessed in Python as a dictionary of key/value pairs (try bpy.context.active_object.data.uv_textures.items() in Blender's Python console). This would be why the array re-ordering techniques fail to work.

I'm not sure that this is the best way but it appears to work. Test to see if it fixes the export order.

import bpy

mesh = bpy.context.active_object.data

mesh.uv_textures.active_index = 0
tmpuvmap = mesh.uv_textures.active
tmpuvmap_name = tmpuvmap.name

newuvmap = mesh.uv_textures.new()
mesh.uv_textures.remove(tmpuvmap)
newuvmap.name = tmpuvmap_name


By setting active_index = 0, the call to new() duplicates the first UVMap, putting a duplicate of it at the end before deleting the first item.

This appears to give the same result as manually selecting the first item, clicking + to create a new UVMap then deleting the first item within blender.